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add more software to jats list, repository column
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castedo committed Apr 11, 2024
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Expand Up @@ -15,7 +15,7 @@ JATS XML Specifications/Recommendations:

A corpus of JATS XML articles embodies a particular "dialect" of JATS XML.

Archived Corpora:
Publicly Archived Corpora of JATS XML:

* **PMC XML**: [PubMed Central (PMC) Open Access Subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/)
* **eLife XML**: [eLife article XML repository](https://github.com/elifesciences/elife-article-xml)
Expand All @@ -30,46 +30,79 @@ Non-archived Corpora:

<table markdown>
<tr>
<th>XML Articles Parsed</th>
<th>Article Repository</th>
<th>XML Parsing Context</th>
<th>Software</th>
<th>Language</th>
</tr>
<tr markdown>
<td>PubMed Central (HTML generation)</td>
<tr>
<td>PubMed Central</td>
<td>?</td>
<td>?</td>
<td></td>
</tr>
<tr markdown>
<td>Europe PMC (HTML generation)</td>
<td>? <a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/full-text-xsl">full-text-xsl</a></td>
<td>JavaScript ? (and XSL)</td>
<tr>
<td>PubMed Central</td>
<td>PubReader (discontinued 2024)</td>
<td><a href="https://github.com/ncbi/PubReader">PubReader</a></td>
<td>JavaScript + XSL</td>
</tr>
<tr markdown>
<td>bioRxiv JATS XML to eLife Reviewed Preprints</td>
<tr>
<td>Europe PMC </td>
<td>HTML generation</td>
<td><a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/full-text-xsl">full-text-xsl</a> + closed-source</td>
<td>XSL + JavaScript</td>
</tr>
<tr>
<td>Europe PMC</td>
<td>internal workflow after manuscript submission</td>
<td> <a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/full-text-xsl">full-text-xsl</a>
+ <a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/xpub-epmc">xpub-epmc</a>
</td>
<td>XSL</td>
</tr>
<tr>
<td>eLife Reviewed Preprints</td>
<td>ingestion of bioRxiv JATS XML</td>
<td><a href="https://github.com/stencila/encoda">Encoda</a></td>
<td>TypeScript</td>
</tr>
<tr>
<td>Servers using Open Preprint Systems (OPS)</td>
<td>?</td>
<td><a href="https://pkp.sfu.ca/software/ops/">OPS</a></td>
<td>PHP</td>
</tr>
<tr>
<td>Journals using Open Journal Systems (OJS)</td>
<td>?</td>
<td><a href="https://github.com/pkp">OJS</a></td>
<td>PHP</td>
</tr>
<tr markdown>
<td>American Mathematical Society (AMS) articles</td>
<td>American Mathematical Society (AMS) journals</td>
<td>internal workflow</td>
<td markdown>
[AMS texml-to-html](https://github.com/AmerMathSoc/texml-to-html)
</td>
<td>JavaScript</td>
</tr>
<tr markdown>
<td>Articles of journals using Open Journal Systems (OJS)</td>
<td><a href="https://github.com/pkp">OJS</a></td>
<td>PHP</td>
</tr>
<tr>
<td>Articles of some journals hosted by <a href="https://www.centre-mersenne.org">Centre Mersenne</a></td>
<td>Some journals hosted by <a href="https://www.centre-mersenne.org">Centre Mersenne</a></td>
<td>ingestion of article data and text into database</td>
<td><a href="https://gricad-gitlab.univ-grenoble-alpes.fr/mathdoc/ptf">MathDoc platform</a></td>
<td>Python</td>
</tr>
<tr>
<td>?</td>
<td>HTML generation</td>
<td><a href="https://github.com/scieloorg/packtools">packtools</a></td>
<td>Python + XSL</td>
</tr>
<tr>
<td>?</td>
<td>HTML generation</td>
<td>eLife Lens and derivatives</td>
<td>JavaScript</td>
</tr>
</table>

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